Human cancer cell proteomics identifies proteins that fail to be degraded upon treatment with a selective autophagy inhibitor

To identify the subproteome degraded by lysosomes in human cancer cells, we compared whole cell proteomes of wild-type and autophagy-deficient non-small cell lung cancer cells in the presence or absence of a lysosomal degradation inhibitor (N/L). Further, we compared whole cell proteomes of cells treated with a selective autophagy inhibitor in the presence or absence of N/L to identify lysosome substrate proteins that fail to be degraded upon treatment with this small molecule.